SoroushVahidi/scidocs huggingface dataset:
Gal4 in the Drosophila female germline
(1998)

The modular Gal4 system has proven to be an extremely useful tool for conditional gene expression in Drosophila. One limitation has been the inability of the system to work in the female germline. A modified Gal4 system that works throughout oogenesis is presented here. To achieve germline expression, it was critical to change the basal promoter and 3'-UTR in the Gal4-responsive expression vector (generating UASp). Basal promoters and heterologous 3'-UTRs are often considered neutral, but as shown here, can endow qualitative tissue-specificity to a chimeric transcript. The modified Gal4 system was used to investigate the role of the Drosophila FGF homologue branchless, ligand for the FGF receptor breathless, in border cell migration. FGF signaling guides tracheal cell migration in the embryo. However, misexpression of branchless in the ovary had no effect on border cell migration. Thus border cells and tracheal cells appear to be guided differently.
Improving Relation Extraction by Pre-trained Language Representations
(2018)

Current state-of-the-art relation extraction methods typically rely on a set of lexical, syntactic, and semantic features, explicitly computed in a pre-processing step. Training feature extraction models requires additional annotated language resources, which severely restricts the applicability and portability of relation extraction to novel languages. Similarly, pre-processing introduces an additional source of error. To address these limitations, we introduce TRE, a Transformer for Relation Extraction. Unlike previous relation extraction models, TRE uses pre-trained deep language representations instead of explicit linguistic features to inform the relation classification and combines it with the self-attentive Transformer architecture to effectively model long-range dependencies between entity mentions. TRE allows us to learn implicit linguistic features solely from plain text corpora by unsupervised pre-training, before fine-tuning the learned language representations on the relation extraction task. TRE obtains a new state-of-the-art result on the TACRED and SemEval 2010 Task 8 datasets, achieving a test F1 of 67.4 and 87.1, respectively. Furthermore, we observe a significant increase in sample efficiency. With only 20% of the training examples, TRE matches the performance of our baselines and our model trained from scratch on 100% of the TACRED dataset. We open-source our trained models, experiments, and source code.
Plate-laminated corporate-feed slotted waveguide array antenna at 350-GHz band by silicon process
(2016)

A corporate feed slotted waveguide array antenna with broadband characteristics in term of gain in the 350 GHz band is achieved by measurement for the first time. The etching accuracy for thin laminated plates of the diffusion bonding process with conventional chemical etching is limited to ±20μm. This limits the use of this process for antenna fabrication in the submillimeter wave band where the fabrication tolerances are very severe. To improve the etching accuracy of the thin laminated plates, a new fabrication process has been developed. Each silicon wafer is etched by DRIE (deep reactive ion etcher) and is plated by gold on the surface. This new fabrication process provides better fabrication tolerances about ±5 μm using wafer bond aligner. The thin laminated wafers are then bonded with the diffusion bonding process under high temperature and high pressure. To validate the proposed antenna concepts, an antenna prototype has been designed and fabricated in the 350 GHz band. The 3dB-down gain bandwidth is about 44.6 GHz by this silicon process while it was about 15GHz by the conventional process using metal plates in measurement.
Private Empirical Risk Minimization: Efficient Algorithms and Tight Error Bounds
(2014)

Convex empirical risk minimization is a basic tool in machine learning and statistics. We provide new algorithms and matching lower bounds for differentially private convex empirical risk minimization assuming only that each data point's contribution to the loss function is Lipschitz and that the domain of optimization is bounded. We provide a separate set of algorithms and matching lower bounds for the setting in which the loss functions are known to also be strongly convex. Our algorithms run in polynomial time, and in some cases even match the optimal nonprivate running time (as measured by oracle complexity). We give separate algorithms (and lower bounds) for (ε, 0)and (ε, δ)-differential privacy; perhaps surprisingly, the techniques used for designing optimal algorithms in the two cases are completely different. Our lower bounds apply even to very simple, smooth function families, such as linear and quadratic functions. This implies that algorithms from previous work can be used to obtain optimal error rates, under the additional assumption that the contributions of each data point to the loss function is smooth. We show that simple approaches to smoothing arbitrary loss functions (in order to apply previous techniques) do not yield optimal error rates. In particular, optimal algorithms were not previously known for problems such as training support vector machines and the high-dimensional median.
Exposure: A Passive DNS Analysis Service to Detect and Report Malicious Domains
(2014)

A wide range of malicious activities rely on the domain name service (DNS) to manage their large, distributed networks of infected machines. As a consequence, the monitoring and analysis of DNS queries has recently been proposed as one of the most promising techniques to detect and blacklist domains involved in malicious activities (e.g., phishing, spam, botnets command-and-control, etc.). EXPOSURE is a system we designed to detect such domains in real time, by applying 15 unique features grouped in four categories.
 We conducted a controlled experiment with a large, real-world dataset consisting of billions of DNS requests. The extremely positive results obtained in the tests convinced us to implement our techniques and deploy it as a free, online service. In this article, we present the Exposure system and describe the results and lessons learned from 17 months of its operation. Over this amount of time, the service detected over 100K malicious domains. The statistics about the time of usage, number of queries, and target IP addresses of each domain are also published on a daily basis on the service Web page.
Practical privacy: the SuLQ framework
(2005)

We consider a statistical database in which a trusted administrator introduces noise to the query responses with the goal of maintaining privacy of individual database entries. In such a database, a query consists of a pair (S, f) where S is a set of rows in the database and f is a function mapping database rows to {0, 1}. The true answer is ΣiεS f(di), and a noisy version is released as the response to the query. Results of Dinur, Dwork, and Nissim show that a strong form of privacy can be maintained using a surprisingly small amount of noise -- much less than the sampling error -- provided the total number of queries is sublinear in the number of database rows. We call this query and (slightly) noisy reply the SuLQ (Sub-Linear Queries) primitive. The assumption of sublinearity becomes reasonable as databases grow increasingly large.We extend this work in two ways. First, we modify the privacy analysis to real-valued functions f and arbitrary row types, as a consequence greatly improving the bounds on noise required for privacy. Second, we examine the computational power of the SuLQ primitive. We show that it is very powerful indeed, in that slightly noisy versions of the following computations can be carried out with very few invocations of the primitive: principal component analysis, k means clustering, the Perceptron Algorithm, the ID3 algorithm, and (apparently!) all algorithms that operate in the in the statistical query learning model [11].
Differentially Private Empirical Risk Minimization
(2011)

Privacy-preserving machine learning algorithms are crucial for the increasingly common setting in which personal data, such as medical or financial records, are analyzed. We provide general techniques to produce privacy-preserving approximations of classifiers learned via (regularized) empirical risk minimization (ERM). These algorithms are private under the ε-differential privacy definition due to Dwork et al. (2006). First we apply the output perturbation ideas of Dwork et al. (2006), to ERM classification. Then we propose a new method, objective perturbation, for privacy-preserving machine learning algorithm design. This method entails perturbing the objective function before optimizing over classifiers. If the loss and regularizer satisfy certain convexity and differentiability criteria, we prove theoretical results showing that our algorithms preserve privacy, and provide generalization bounds for linear and nonlinear kernels. We further present a privacy-preserving technique for tuning the parameters in general machine learning algorithms, thereby providing end-to-end privacy guarantees for the training process. We apply these results to produce privacy-preserving analogues of regularized logistic regression and support vector machines. We obtain encouraging results from evaluating their performance on real demographic and benchmark data sets. Our results show that both theoretically and empirically, objective perturbation is superior to the previous state-of-the-art, output perturbation, in managing the inherent tradeoff between privacy and learning performance.
Differentially Private Distributed Constrained Optimization
(2017)

Many resource allocation problems can be formulated as an optimization problem whose constraints contain sensitive information about participating users. This paper concerns a class of resource allocation problems whose objective function depends on the aggregate allocation (i.e., the sum of individual allocations); in particular, we investigate distributed algorithmic solutions that preserve the privacy of participating users. Without privacy considerations, existing distributed algorithms normally consist of a central entity computing and broadcasting certain public coordination signals to participating users. However, the coordination signals often depend on user information, so that an adversary who has access to the coordination signals can potentially decode information on individual users and put user privacy at risk. We present a distributed optimization algorithm that preserves differential privacy, which is a strong notion that guarantees user privacy regardless of any auxiliary information an adversary may have. The algorithm achieves privacy by perturbing the public signals with additive noise, whose magnitude is determined by the sensitivity of the projection operation onto user-specified constraints. By viewing the differentially private algorithm as an implementation of stochastic gradient descent, we are able to derive a bound for the suboptimality of the algorithm. We illustrate the implementation of our algorithm via a case study of electric vehicle charging. Specifically, we derive the sensitivity and present numerical simulations for the algorithm. Through numerical simulations, we are able to investigate various aspects of the algorithm when being used in practice, including the choice of step size, number of iterations, and the trade-off between privacy level and suboptimality.
The role of transparency in recommender systems
(2002)

Recommender Systems act as a personalized decision guides, aiding users in decisions on matters related to personal taste. Most previous research on Recommender Systems has focused on the statistical accuracy of the algorithms driving the systems, with little emphasis on interface issues and the user's perspective. The goal of this research was to examine the role of transprency (user understanding of why a particular recommendation was made) in Recommender Systems. To explore this issue, we conducted a user study of five music Recommender Systems. Preliminary results indicate that users like and feel more confident about recommendations that they perceive as transparent.
Recognizing Abnormal Heart Sounds Using Deep Learning
(2017)

The work presented here applies deep learning to the task of automated cardiac auscultation, i.e. recognizing abnormalities in heart sounds. We describe an automated heart sound classification algorithm that combines the use of time-frequency heat map representations with a deep convolutional neural network (CNN). Given the cost-sensitive nature of misclassification, our CNN architecture is trained using a modified loss function that directly optimizes the trade-off between sensitivity and specificity. We evaluated our algorithm at the 2016 PhysioNet Computing in Cardiology challenge where the objective was to accurately classify normal and abnormal heart sounds from single, short, potentially noisy recordings. Our entry to the challenge achieved a final specificity of 0.95, sensitivity of 0.73 and overall score of 0.84. We achieved the greatest specificity score out of all challenge entries and, using just a single CNN, our algorithm differed in overall score by only 0.02 compared to the top place finisher, which used an ensemble approach.
The Tire as an Intelligent Sensor
(2009)

Active safety systems are based upon the accurate and fast estimation of the value of important dynamical variables such as forces, load transfer, actual tire-road friction (kinetic friction) muk, and maximum tire-road friction available (potential friction) mup. Measuring these parameters directly from tires offers the potential for improving significantly the performance of active safety systems. We present a distributed architecture for a data-acquisition system that is based on a number of complex intelligent sensors inside the tire that form a wireless sensor network with coordination nodes placed on the body of the car. The design of this system has been extremely challenging due to the very limited available energy combined with strict application requirements for data rate, delay, size, weight, and reliability in a highly dynamical environment. Moreover, it required expertise in multiple engineering disciplines, including control-system design, signal processing, integrated-circuit design, communications, real-time software design, antenna design, energy scavenging, and system assembly.
Surgical precision JIT compilers
(2014)

Just-in-time (JIT) compilation of running programs provides more optimization opportunities than offline compilation. Modern JIT compilers, such as those in virtual machines like Oracle's HotSpot for Java or Google's V8 for JavaScript, rely on dynamic profiling as their key mechanism to guide optimizations. While these JIT compilers offer good average performance, their behavior is a black box and the achieved performance is highly unpredictable.
 In this paper, we propose to turn JIT compilation into a precision tool by adding two essential and generic metaprogramming facilities: First, allow programs to invoke JIT compilation explicitly. This enables controlled specialization of arbitrary code at run-time, in the style of partial evaluation. It also enables the JIT compiler to report warnings and errors to the program when it is unable to compile a code path in the demanded way. Second, allow the JIT compiler to call back into the program to perform compile-time computation. This lets the program itself define the translation strategy for certain constructs on the fly and gives rise to a powerful JIT macro facility that enables "smart" libraries to supply domain-specific compiler optimizations or safety checks.
 We present Lancet, a JIT compiler framework for Java bytecode that enables such a tight, two-way integration with the running program. Lancet itself was derived from a high-level Java bytecode interpreter: staging the interpreter using LMS (Lightweight Modular Staging) produced a simple bytecode compiler. Adding abstract interpretation turned the simple compiler into an optimizing compiler. This fact provides compelling evidence for the scalability of the staged-interpreter approach to compiler construction.
 In the case of Lancet, JIT macros also provide a natural interface to existing LMS-based toolchains such as the Delite parallelism and DSL framework, which can now serve as accelerator macros for arbitrary JVM bytecode.
An LDA-Based Approach to Scientific Paper Recommendation
(2016)

Recommendation of scientific papers is a task aimed to support researchers in accessing relevant articles from a large pool of unseen articles. When writing a paper, a researcher focuses on the topics related to her/his scientific domain, by using a technical language. The core idea of this paper is to exploit the topics related to the researchers scientific production (authored articles) to formally define her/his profile; in particular we propose to employ topic modeling to formally represent the user profile, and language modeling to formally represent each unseen paper. The recommendation technique we propose relies on the assessment of the closeness of the language used in the researchers papers and the one employed in the unseen papers. The proposed approach exploits a reliable knowledge source for building the user profile, and it alleviates the cold-start problem, typical of collaborative filtering techniques. We also present a preliminary evaluation of our approach on the DBLP.
Adaptive Laplace Mechanism: Differential Privacy Preservation in Deep Learning
(2017)

In this paper, we focus on developing a novel mechanism to preserve differential privacy in deep neural networks, such that: (1) The privacy budget consumption is totally independent of the number of training steps; (2) It has the ability to adaptively inject noise into features based on the contribution of each to the output; and (3) It could be applied in a variety of different deep neural networks. To achieve this, we figure out a way to perturb affine transformations of neurons, and loss functions used in deep neural networks. In addition, our mechanism intentionally adds "more noise" into features which are "less relevant" to the model output, and vice-versa. Our theoretical analysis further derives the sensitivities and error bounds of our mechanism. Rigorous experiments conducted on MNIST and CIFAR-10 datasets show that our mechanism is highly effective and outperforms existing solutions.
Why do you play World of Warcraft? An in-depth exploration of self-reported motivations to play online and in-game behaviours in the virtual world of Azeroth
(2013)

Massively multiplayer online role-playing games (MMORPGs) are video games in which players create an avatar that evolves and interacts with other avatars in a persistent virtual world. Motivations to play MMORPGs are heterogeneous (e.g. achievement, socialisation, immersion in virtual worlds). This study investigates in detail the relationships between self-reported motives and actual in-game behaviours. We recruited a sample of 690 World of Warcraft players (the most popular MMORPG) who agreed to have their avatar monitored for 8 months. Participants completed an initial online survey about their motives to play. Their actual in-game behaviours were measured through the game’s official database (the Armory website). Results showed specific associations between motives and in-game behaviours. Moreover, longitudinal analyses revealed that teamworkand competition-oriented motives are the most accurate predictors of fast progression in the game. In addition, although specific associations exist between problematic use and certain motives (e.g. advancement, escapism), longitudinal analyses showed that high involvement in the game is not necessarily associated with a negative impact upon daily living. 2012 Elsevier Ltd. All rights reserved.
Policy ratification
(2005)

It is not sufficient to merely check the syntax of new policies before they are deployed in a system; policies need to be analyzed for their interactions with each other and with their local environment. That is, policies need to go through a ratification process. We believe policy ratification becomes an essential part of system management as the number of policies in the system increases and as the system administration becomes more decentralized. In this paper, we focus on the basic tasks involved in policy ratification. To a large degree, these basic tasks can be performed independent of policy model and language and require little domain-specific knowledge. We present algorithms from constraint, linear, and logic programming disciplines to help perform ratification tasks. We provide an algorithm to efficiently assign priorities to the policies based on relative policy preferences indicated by policy administrators. Finally, with an example, we show how these algorithms have been integrated with our policy system to provide feedback to a policy administrator regarding potential interactions of policies with each other and with their deployment environment.
Centrality in valued graphs : A measure of betweenness based on network flow
(1991)

A new measure of centrality, C,, is introduced. It is based on the concept of network flows. While conceptually similar to Freeman’s original measure, Ca, the new measure differs from the original in two important ways. First, C, is defined for both valued and non-valued graphs. This makes C, applicable to a wider variety of network datasets. Second, the computation of C, is not based on geodesic paths as is C, but on all the independent paths between all pairs of points in the network.
Distributed Energy Resources Topology Identification via Graphical Modeling
(2017)

Distributed energy resources (DERs), such as photovoltaic, wind, and gas generators, are connected to the grid more than ever before, which introduces tremendous changes in the distribution grid. Due to these changes, it is important to understand where these DERs are connected in order to sustainably operate the distribution grid. But the exact distribution system topology is difficult to obtain due to frequent distribution grid reconfigurations and insufficient knowledge about new components. In this paper, we propose a methodology that utilizes new data from sensor-equipped DER devices to obtain the distribution grid topology. Specifically, a graphical model is presented to describe the probabilistic relationship among different voltage measurements. With power flow analysis, a mutual information-based identification algorithm is proposed to deal with tree and partially meshed networks. Simulation results show highly accurate connectivity identification in the IEEE standard distribution test systems and Electric Power Research Institute test systems.
Performance of Reliable Transport Protocol over IEEE 802.11 Wireless LAN: Analysis and Enhancement
(2002)

IEEE 802.11 Medium Access Control(MAC) is proposed to support asynchronous and time bounded delivery of radio data packets in infrastructure and ad hoc networks. The basis of the IEEE 802.11 WLAN MAC protocol is Distributed Coordination Function(DCF), which is a Carrier Sense Multiple Access with Collision Avoidance(CSMA/CA) with binary slotted exponential back-off scheme. Since IEEE 802.11 MAC has its own characteristics that are different from other wireless MAC protocols, the performance of reliable transport protocol over 802.11 needs further study. This paper proposes a scheme named DCF+, which is compatible with DCF, to enhance the performance of reliable transport protocol over WLAN. To analyze the performance of DCF and DCF+, this paper also introduces an analytical model to compute the saturated throughput of WLAN. Comparing with other models, this model is shown to be able to predict the behaviors of 802.11 more accurately. Moreover, DCF+ is able to improve the performance of TCP over WLAN, which is verified by modeling and elaborate simulation results.